SF BAY ECOSYSTEM COLLAPSING AS RIVERS DIVERTED, SCIENTISTS REPORT...

A barge is anchored at Rock Slough in Brentwood. A study shows a dramatic decrease in river water levels flowing into the bay. Photo: Paul Chinn, The Chronicle

WASHINGTON — Evidence of what scientists are calling the planet’s Sixth Mass Extinction is appearing in San Francisco Bay and its estuary, the largest on the Pacific Coast of North and South America, according to a major new study...

So little water is flowing from the rivers that feed the estuary, which includes the Sacramento-San Joaquin River Delta, Suisun Marsh and the bay, that its ecosystem is collapsing, scientists who conducted the study say.

Human extraction of water from the rivers is not only pushing the delta smelt toward extinction, they say, but also threatening dozens more fish species and many birds and marine mammals, including orca whales, that depend on the estuary’s complex food web.

The findings by scientists at the Bay Institute, an environmental group, underline conclusions already reached by state regulators and are intended to buttress the environmental case for potentially drastic water restrictions in San Francisco and other parts of the Bay Area, and among farmers in the northern San Joaquin Valley.

The State Water Resources Control Board moved last month to require that Californians leave far more water — 40 percent of what would naturally flow during spring — in the San Joaquin River and its three main tributaries, the Tuolumne, Merced and Stanislaus rivers, in an effort to save fish species.

That would double the amount of water protected from human use in most years, according to the board. Last year, only 10 percent of the San Joaquin River, the second-largest in the state, reached the delta, as the rest was diverted or stored upstream. The Tuolumne, which is San Francisco’s main water supply, is one of the state’s most over-tapped rivers, with about 80 percent of its normal flow directed to human uses.

Jon Rosenfield, the lead scientist on the Bay Institute report, said people take so much water from the rivers that the estuary’s entire ecosystem is in collapse.

“Our estuary is being choked” by a lack of fresh water, Rosenfield said. Over the past four decades, he said, urban users and farmers have diverted so much water from the rivers that in all but the wettest years, severe drought has become a permanent condition for wildlife.

UC Davis fish biologist Peter Moyle, who is not connected with the study and had not viewed its results, confirmed in a telephone interview that native fish species in the estuary face dire conditions.

“You don’t have to look far to find documentation of the Sixth Extinction,” Moyle said. “It’s happening now in California.”

Moyle said that of the roughly 120 native freshwater fish species in California, “over 80 percent of those are faced with extinction by the end of the century if current trends continue.”

“I always tell people there’s always going to be an ecosystem out there; it just may not be one we like,” Moyle said, “and it’s increasingly headed in that direction.”

The study, which was sponsored by the San Francisco Estuary Partnership, a quasi-governmental agency, found that lack of freshwater flows, especially during the ecologically critical winter and spring months, has had profound effects. These include:

•Looming fish extinctions. In addition to the delta smelt, which farmers often blame for water cutbacks, five other native fish species are severely endangered. Among them are two runs of chinook salmon, longfin smelt, green sturgeon and Central Valley steelhead. Dozens of others, such as fall run chinook salmon, white sturgeon and the Sacramento splittail, are in severe decline, listed currently as “species of concern.”

•Starvation of fish-dependent species. Orca whales off the coast rely on chinook salmon for food. As salmon populations plummet, the whales are exhibiting signs of food deprivation and reproductive failure. Other marine mammals such as seals and fish-eating birds — pelicans, terns and cormorants — are also affected. Twenty-two species of birds in the estuary are listed as endangered, threatened, or species of concern. Habitat loss is the main stress, but it is compounded by a decline in available food.

•Diminished freshwater to the Gulf of the Farallones. This national marine sanctuary just outside the Golden Gate is a hot spot of marine and avian life fed by a plume of brackish water — part fresh and part saline — that has declined as river flows into the estuary have fallen.

•Increased salinity. Lack of freshwater has harmed zooplankton that lie near the base of the food chain, providing food for fish and birds. Salinity changes encourage invasive species such as the overbite clam, which in turn reduces phytoplankton at the base of the food web.

•Lack of sediment. Reduced river flows mean less sediment is deposited on the bay’s beaches and tidal marshes.

“The bottom line is we’ve simply diverted too much water for fish to be able to survive,” said Felicia Marcus, chair of the State Water Resources Control Board, in announcing the draft rules last month. The board is taking public comment until Nov. 15 and plans to issue final rules next spring.

The board’s 40 percent target for river flows is a third lower than the 60 percent level that the board recommended in 2010. The new target is a compromise to try to help wildlife without imposing draconian cutbacks on cities and farms.

Rosenfield said the 40 percent target is too low and won’t work. “Forty percent isn’t a river,” he said.

But modeling by the San Francisco Public Utilities Commission, which opposes the plan, found that even a smaller target — 35 percent — would lead to water supply cuts of 42 percent to 52 percent in drought years, said commission spokesman Charles Sheehan, who added that up to 188,000 jobs would be lost among the agency’s 2.6 million Bay Area customers.

“It’s hard to see how our community continues to thrive and prosper with that level of water rationing,” Sheehan said.

Chris Scheuring, a lawyer for the California Farm Bureau, a farmer group, said farmers in the northern San Joaquin are expected to put up a stiff fight.

“I hear talk from our membership up on the (tributaries) that they are not in a lay-down mode on this one,” Scheuring said. “It’s just too big for them to not push back.”

Scheuring said that “in a vacuum, a biologist would want all the water back in the river, but that’s just not human reality.”

With close to 40 million people in California, he said, “the idea that we can just sort of stop diverting from our rivers — the argument hardly even needs to be made against it.”

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